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DDX58 DExD/H-box helicase 58 [ Homo sapiens (human) ]

Gene ID: 23586, updated on 10-May-2020

Summary

Official Symbol
DDX58provided by HGNC
Official Full Name
DExD/H-box helicase 58provided by HGNC
Primary source
HGNC:HGNC:19102
See related
Ensembl:ENSG00000107201 MIM:609631
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RIG1; RIGI; RIG-I; RLR-1; SGMRT2
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases which are implicated in a number of cellular processes involving RNA binding and alteration of RNA secondary structure. This gene encodes a protein containing RNA helicase-DEAD box protein motifs and a caspase recruitment domain (CARD). It is involved in viral double-stranded (ds) RNA recognition and the regulation of immune response. [provided by RefSeq, Jul 2008]
Annotation information
Note: RARRES3 (Gene ID: 5920) and DDX58 (Gene ID: 23586) share the RIG1/RIG-1 alias in common. RIG1 is a widely used alternative name for DExD/H-box helicase 58 (DDX58), which can be confused with the retinoic acid receptor responder 3 (RARRES3) gene, since they share the same alias. [22 Jan 2019]
Expression
Ubiquitous expression in appendix (RPKM 7.8), spleen (RPKM 7.4) and 25 other tissues See more
Orthologs

Genomic context

See DDX58 in Genome Data Viewer
Location:
9p21.1
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (32455302..32526196, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (32455300..32526322, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987059 Neighboring gene Sharpr-MPRA regulatory region 8424 Neighboring gene aconitase 1 Neighboring gene TOP1 binding arginine/serine rich protein, E3 ubiquitin ligase Neighboring gene small integral membrane protein 27 Neighboring gene NADH:ubiquinone oxidoreductase subunit B6 Neighboring gene DNA fragmentation factor subunit beta pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vpr vpr HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived dendritic cells PubMed
vpr HIV-1 Vpr upregulates the gene expression of DDX58 in human monocyte-derived macrophages PubMed
retropepsin gag-pol HIV-1 PR targets and relocalizes RIG-I to an insoluble membrane fraction followed by lysosome-mediated degradation PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: TOPORS

Homology

Clone Names

  • FLJ13599, DKFZp434J1111, DKFZp686N19181

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA helicase activity IEA
Inferred from Electronic Annotation
more info
 
double-stranded DNA binding IEA
Inferred from Electronic Annotation
more info
 
double-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-stranded RNA binding TAS
Traceable Author Statement
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
single-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
single-stranded RNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
ubiquitin protein ligase binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
zinc ion binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
RIG-I signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
RIG-I signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to exogenous dsRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
cytoplasmic pattern recognition receptor signaling pathway in response to virus TAS
Traceable Author Statement
more info
PubMed 
defense response to virus IDA
Inferred from Direct Assay
more info
PubMed 
defense response to virus TAS
Traceable Author Statement
more info
 
detection of virus IDA
Inferred from Direct Assay
more info
PubMed 
innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
innate immune response IMP
Inferred from Mutant Phenotype
more info
PubMed 
innate immune response TAS
Traceable Author Statement
more info
 
negative regulation of type I interferon production TAS
Traceable Author Statement
more info
 
positive regulation of DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of defense response to virus by host IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of granulocyte macrophage colony-stimulating factor production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-alpha production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-alpha production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-alpha secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-beta production IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interferon-beta production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interferon-beta production IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-beta secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-6 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of interleukin-6 secretion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of interleukin-6 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-8 production IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of myeloid dendritic cell cytokine production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of response to cytokine stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of tumor necrosis factor secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
regulation of type III interferon production TAS
Traceable Author Statement
more info
PubMed 
response to exogenous dsRNA ISS
Inferred from Sequence or Structural Similarity
more info
 
response to virus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to virus TAS
Traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
bicellular tight junction IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
ruffle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
antiviral innate immune response receptor RIG-I
Names
DEAD (Asp-Glu-Ala-Asp) box polypeptide 58
DEAD box protein 58
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide
RNA helicase RIG-I
probable ATP-dependent RNA helicase DDX58
retinoic acid-inducible gene 1 protein
retinoic acid-inducible gene I protein
NP_055129.2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_046918.1 RefSeqGene

    Range
    5129..76023
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_014314.4NP_055129.2  antiviral innate immune response receptor RIG-I

    See identical proteins and their annotated locations for NP_055129.2

    Status: REVIEWED

    Source sequence(s)
    AA862613, AF038963, AL161783, BC070029, DN998145
    Consensus CDS
    CCDS6526.1
    UniProtKB/Swiss-Prot
    O95786
    Related
    ENSP00000369213.2, ENST00000379883.3
    Conserved Domains (4) summary
    cd08817
    Location:100189
    CARD_RIG-I_r2; Caspase activation and recruitment domain found in RIG-I, second repeat
    cd15805
    Location:805918
    RIG-I_C; C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor
    cl14633
    Location:292
    DD; Death Domain Superfamily of protein-protein interaction domains
    cl17041
    Location:243771
    helicase_insert_domain; helicase_insert_domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    32455302..32526196 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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